protected MnaseOutput countMnaseReads(
String chr,
int pos,
ChromScoresFast fwCounts,
ChromScoresFast revCounts,
boolean chipSeqMetric)
throws Exception {
double PSEUDOCOUNT = 0.005; // per bp
int FRAGLENHIGH = 600;
int center = pos;
int quarterNuc = (int) ((double) this.footprintSize / 4.0);
int halfNuc = (int) ((double) this.footprintSize / 2.0);
int assocHalf = (int) ((double) this.assocSize / 2.0);
int fraghalf = (int) ((double) FRAGLENHIGH / 2.0);
int cycle = halfNuc;
int s, e;
MnaseOutput out = new MnaseOutput();
// int windHalf = (int)((double)this.normalizationWindow/2.0);
// s = center - windHalf;
// e = center + windHalf;
// out.normWindCount = (double)this.countUnstrandedReads(fwCounts, revCounts,chr, s, e);
// // System.err.printf("NormWind Cpg %d\t Getting (all) reads %s at %d-%d\t%d\n", center,
// mnasePrefix, s, e,(int)normWindCount);
if (chipSeqMetric) {
// CHIP-SEQ . THIS SHOULD TAKE A FRAGMENT LEN, BUT 600 is based on K4 IMR90 offsets.
System.err.println("Why are we using ChIP-seq metric??");
System.exit(1);
// First fw
s = center - fraghalf;
e = center;
int preCountPos = countReads(fwCounts, chr, s, e);
// if (preCountPos>0) System.err.printf("Cpg %d\t Getting (+) reads at %d-%d\t%d\n", center,
// s, e,preCountPos);
// Then rev
s = center;
e = center + fraghalf;
int postCountNeg = countReads(revCounts, chr, s, e);
// if (postCountNeg>0) System.err.printf("Cpg %d\t Getting (-) reads at %d-%d\t%d\n", center,
// s, e,postCountNeg);
out.val = (double) (preCountPos + postCountNeg) / (double) fraghalf;
out.rawCounts = preCountPos + postCountNeg;
// if (this.normalizationWindow>0.0)
// {
// out = ((double)(preCountPos+postCountNeg)+(PSEUDOCOUNT*(double)fraghalf)) *
// (1.0/((double)normWindCount+(PSEUDOCOUNT*(double)this.normalizationWindow))) *
// (((double)this.normalizationWindow)/((double)fraghalf));
// out = Math.log(out)/LOG_OF_TWO;
// }
} else {
// MNASE METRIC
// First fw
s = center - cycle - assocHalf;
e = center - cycle + assocHalf;
int preCountPos = countReads(fwCounts, chr, s, e);
// System.err.printf("Cpg %d\t Getting (+) reads at %d-%d\t%d\n", center, s, e,preCountPos);
// Then rev
s = center + cycle - assocHalf;
e = center + cycle + assocHalf;
int postCountNeg = countReads(revCounts, chr, s, e);
// System.err.printf("Cpg %d\t Getting (-) reads at %d-%d\t%d\n", center, s, e,postCountNeg);
int phasedCount = preCountPos + postCountNeg;
int phasedLen = 2 * assocHalf;
out.rawCounts = phasedCount;
out.val = phasedCount;
// Then unphased
int unphasedCount = 0;
s = center - assocHalf;
e = center + assocHalf;
unphasedCount += countUnstrandedReads(fwCounts, revCounts, chr, s, e);
int unphasedLen = 2 * assocHalf;
// s = center - this.PERIODICITY - assocHalf;
// e = center - this.PERIODICITY + assocHalf;
// unphasedCount += countUnstrandedReads(fwCounts, revCounts, chr, s, e);
// s = center + this.PERIODICITY - assocHalf;
// e = center + this.PERIODICITY + assocHalf;
// unphasedCount += countUnstrandedReads(fwCounts, revCounts, chr, s, e);
// int unphasedLen = 6 * assocHalf;
// // System.err.printf("Cpg %d\t Getting unphased reads at %d-%d\t%d\n", center, center -
// this.PERIODICITY - assocHalf,
// // center + this.PERIODICITY + assocHalf,unphasedCount);
//
//
//
out.val =
((double) (phasedCount) + (PSEUDOCOUNT * (double) phasedLen))
* (1.0 / ((double) unphasedCount + (PSEUDOCOUNT * (double) unphasedLen)))
* (((double) unphasedLen) / ((double) phasedLen));
out.val = Math.log(out.val) / LOG_OF_TWO;
out.val = phasedCount - unphasedCount;
out.val = Math.min(preCountPos, postCountNeg) - unphasedCount;
}
return out;
}
